Understanding the Output

• The label field is printed to the top left corner of the diagram. In the absence of an explicit label, the partition function free energy is reported (here G=-11.0145 kcal/mol). The MFE free energy is reported in red (here G=-9.9 kcal/mol).
• The line thickness of each arc is proportional to the probability of forming a base pair between the two bases. Arcs that are darker and thicker represent base pairs with a higher likelihood of bonding.
• In this example you can see that another structure is in equilibrium with the MFE macrostate. You may wish to use the clusterRNAbow tool to resolve those two clusters.